1YFI | PD0621 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE MSPI IN COMPLEX WITH ITS COGNATE DNA IN P212121 SPACE GROUP

Authors :   Q. S. Xu, R. B. Kucera, R. J. Roberts, H. -C. Guo

Date :   02 Jan 05 (Deposition) - 10 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,D  (1x)
Biol. Unit 2: B,E,F  (1x)

Keywords :   Protein-Dna Complex, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. S. Xu, R. J. Roberts, H. -C. Guo
Two Crystal Forms Of The Restriction Enzyme Mspi-Dna Complex Show The Same Novel Structure.
Protein Sci. V. 14 2590 2005
PubMed-ID: 16195548 | Reference-DOI: 10.1110/PS.051565105
(for further references see the PDB file header)

*Molecule 1 - 5'-D(CPCPCPCPCPGPGPGPGPG)-3'*
	Chains	:	C, D, E, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - TYPE II RESTRICTION ENZYME MSPI
	Chains	:	A, B
	EC Number	:	3.1.21.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCAD39
	Expression System Strain	:	ER2502
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MSPIR
	Organism Scientific	:	MORAXELLA SP.
	Organism Taxid	:	479
	Synonym	:	ENDONUCLEASE MSPI, R.MSPI

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A		C	D
Biological Unit 2 (1x)	:		B			E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1YFI)

(no "Site" information available for 1YFI)

(no "SS Bond" information available for 1YFI)

(no "Cis Peptide Bond" information available for 1YFI)

(no "SAP(SNP)/Variant" information available for 1YFI)

(no "PROSITE Motif" information available for 1YFI)

(no "Exon" information available for 1YFI)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:262
 aligned with T2M1_MORSP | P11405 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
           T2M1_MORSP     1 MRTELLSKLYDDFGIDQLPHTQHGVTSDRLGKLYEKYILDIFKDIESLKKYNTNAFPQEKDISSKLLKALNLDLDNIIDVSSSDTDLGRTIAGGSPKTDATIRFTFHNQSSRLVPLNIKHSSKKKVSIAEYDVETICTGVGISDGELKELIRKHQNDQSAKLFTPVQKQRLTELLEPYRERFIRWCVTLRAEKSEGNILHPDLLIRFQVIDREYVDVTIKNIDDYVSDRIAEGSKARKPGFGTGLNWTYASGSKAKKMQFKG 262
               SCOP domains d1yfia_ A: Restriction endonuclease MspI                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhh..hhh.eeeeeeee...............eeeeeee....eeeeeeeeeee....eeeeeehhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhh.............eeeeeeee..eeeeeeeeehhhhhhhhhhhh....hhhhhh..eeee........eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yfi A   1 MRTELLSKLYDDFGIDQLPHTQHGVTSDRLGKLYEKYILDIFKDIESLKKYNTNAFPQEKDISSKLLKALNLDLDNIIDVSSSDTDLGRTIAGGSPKTDATIRFTFHNQSSRLVPLNIKHSSKKKVSIAEYDVETICTGVGISDGELKELIRKHQNDQSAKLFTPVQKQRLTELLEPYRERFIRWCVTLRAEKSEGNILHPDLLIRFQVIDREYVDVTIKNIDDYVSDRIAEGSKARKPGFGTGLNWTYASGSKAKKMQFKG 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with T2M1_MORSP | P11405 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
           T2M1_MORSP     1 MRTELLSKLYDDFGIDQLPHTQHGVTSDRLGKLYEKYILDIFKDIESLKKYNTNAFPQEKDISSKLLKALNLDLDNIIDVSSSDTDLGRTIAGGSPKTDATIRFTFHNQSSRLVPLNIKHSSKKKVSIAEYDVETICTGVGISDGELKELIRKHQNDQSAKLFTPVQKQRLTELLEPYRERFIRWCVTLRAEKSEGNILHPDLLIRFQVIDREYVDVTIKNIDDYVSDRIAEGSKARKPGFGTGLNWTYASGSKAKKMQFKG 262
               SCOP domains d1yfib_ B: Restriction endonuclease MspI                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Endonuc-MspI-1yfiB01 B:2-262                                                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) -Endonuc-MspI-1yfiB02 B:2-262                                                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhh..hhh.eeeeeeee...............eeeeeee....eeeeeeeeeee....eeeeeehhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhh.............eeeeeeee..eeeeeeeeehhhhhhhhhhhh....hhhhhh..eeee........eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yfi B   1 MRTELLSKLYDDFGIDQLPHTQHGVTSDRLGKLYEKYILDIFKDIESLKKYNTNAFPQEKDISSKLLKALNLDLDNIIDVSSSDTDLGRTIAGGSPKTDATIRFTFHNQSSRLVPLNIKHSSKKKVSIAEYDVETICTGVGISDGELKELIRKHQNDQSAKLFTPVQKQRLTELLEPYRERFIRWCVTLRAEKSEGNILHPDLLIRFQVIDREYVDVTIKNIDDYVSDRIAEGSKARKPGFGTGLNWTYASGSKAKKMQFKG 262
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain C from PDB  Type:DNA  Length:9
                                         
                 1yfi C   1 CCCCCGGGG   9

Chain D from PDB  Type:DNA  Length:9
                                         
                 1yfi D  12 CCCCGGGGG  20

Chain E from PDB  Type:DNA  Length:10
                                          
                 1yfi E   1 CCCCCGGGGG  10
                                    10

Chain F from PDB  Type:DNA  Length:10
                                          
                 1yfi F  11 CCCCCGGGGG  20
                                    20

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Restriction endonuclease-like (209)

Superfamily: Restriction endonuclease-like (170)

Family: Restriction endonuclease MspI (2)

Protein domain: Restriction endonuclease MspI (2)

Moraxella sp. [TaxId: 479] (2)

1a	d1yfia_	A:
1b	d1yfib_	B:

(no "CATH Domain" information available for 1YFI)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Endonuc-MspI] (2)

Family: Endonuc-MspI (2)

Moraxella sp (2)

1a	Endonuc-MspI-1yfiB01	B:2-262
1b	Endonuc-MspI-1yfiB02	B:2-262

Asymmetric Unit(hide GO term definitions)

Chain A,B (T2M1_MORSP | P11405)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0009036	Type II site-specific deoxyribonuclease activity	Catalysis of the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates and 3' hydroxyls. Cleavage is dependent on the presence in the DNA of a specific recognition site; cleavage occurs at or very near this recognition site.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	GO:0009307	DNA restriction-modification system	A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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	Cis Peptide Bonds
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Biological Units
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	T2M1_MORSP \| P11405	:	1sa3

1sa3	THE SAME ENZYME-DNA COMPLEX IN P21 SPACE GROUP

Description

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